个人学习随笔

下面是我自己最近所学习的知识。

之前自己处理的数据集发现了大问题，现在又重新处理。

关于从pdb数据库中提取一级序列

定义一个PDBparser类，定义parsePrimaryStructure（）函数，用pdbparser.parsePrimaryStructure(file)实现一级序列提取的功能。

 

import json;
    class PDBparser():    
        def parse(self,PDBfile,indent = False):
            '''
            @return: The full information parsed from the PDBFile
            @param PDBFile: The full path of the PDB file, str
            '''
            content = {} # The full information parsed from the PDBFile
            priStructure = content['primary_structure'] = []  # The primary structure parsed from the PDBFile
            tertiary_structure = content['tertiary_structure'] ={}
            terStructure = tertiary_structure['chains'] = [] # The teritary structure parsed from the PDBFile
            #residueindexlist = set()
            lines = self.__loadPDBfile(PDBfile)
            langthinformation = self.__parseLine(lines,content) 
          if indent:
              return content,langthinformation # for test
          else:
              return content
     def parsePrimaryStructure(self,PDBfile):
          '''
          @return: The full information parsed from the PDBFile
          @param PDBFile: The full path of the PDB file, str
          '''
          priStructure = []; # The primary structure parsed from the PDBFile
          lines = self.__loadPDBfile(PDBfile)
          for line in lines:
              header = line.split()[0]
              if header == 'SEQRES':
                  self.__parsePriLine(line, priStructure)
          return priStructure 

定义main函数

 if __name__ == "__main__": 
     print('please input the path of the PDBfile:such as E:\\pdb\\pdb3rum.ent')#输入pdb文件
     file=input()
     pdbparser = PDBparser()
     #content = pdbparser.parseTertiaryStructure(file)
     content = pdbparser.parsePrimaryStructure(file)  
     formatinput = json.dumps(content, indent=1)
     print(formatinput)
     print("Done")